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- PDB-9h6c: Crystal structure of the E. coli F-plasmid VapBC toxin-antitoxin ... -

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Basic information

Entry
Database: PDB / ID: 9h6c
TitleCrystal structure of the E. coli F-plasmid VapBC toxin-antitoxin complex (VapB T3N)
Components
  • Antitoxin
  • tRNA(fMet)-specific endonuclease VapC
KeywordsTOXIN / VapBC / toxin-antitoxin / antibiotic tolerance
Function / homology
Function and homology information


RNA nuclease activity / toxin activity / endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding
Similarity search - Function
: / : / : / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / PIN domain / PIN-like domain superfamily
Similarity search - Domain/homology
Toxin-antitoxin system antitoxin VapB / tRNA(fMet)-specific endonuclease VapC
Similarity search - Component
Biological speciesEscherichia coli KLY (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHollingshead, S. / McVicker, G. / Nielsen, M.R. / Zhang, Y. / Pilla, G. / Jones, R.A. / Thomas, J.C. / Johansen, S.E.H. / Exley, R.M. / Brodersen, D.E. / Tang, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust221924/Z/20/Z United Kingdom
CitationJournal: Mbio / Year: 2025
Title: Shared mechanisms of enhanced plasmid maintenance and antibiotic tolerance mediated by the VapBC toxin:antitoxin system.
Authors: Hollingshead, S. / McVicker, G. / Nielsen, M.R. / Zhang, Y. / Pilla, G. / Jones, R.A. / Thomas, J.C. / Johansen, S.E.H. / Exley, R.M. / Brodersen, D.E. / Tang, C.M.
History
DepositionOct 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA(fMet)-specific endonuclease VapC
B: Antitoxin
C: tRNA(fMet)-specific endonuclease VapC
D: Antitoxin


Theoretical massNumber of molelcules
Total (without water)51,5304
Polymers51,5304
Non-polymers00
Water00
1
A: tRNA(fMet)-specific endonuclease VapC
B: Antitoxin
C: tRNA(fMet)-specific endonuclease VapC
D: Antitoxin

A: tRNA(fMet)-specific endonuclease VapC
B: Antitoxin
C: tRNA(fMet)-specific endonuclease VapC
D: Antitoxin


Theoretical massNumber of molelcules
Total (without water)103,0618
Polymers103,0618
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area26800 Å2
ΔGint-104 kcal/mol
Surface area31920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.974, 88.974, 115.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein tRNA(fMet)-specific endonuclease VapC / RNase VapC / Toxin VapC


Mass: 14818.081 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli KLY (bacteria)
Gene: orf5, vapC, EWK56_24100, F7N46_24920, FGAF1022_52400, FGAS143_47190, G4A38_21190, G4A47_21040
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q84A22, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin / VapB protein (Antitoxin to VapC)


Mass: 10947.062 Da / Num. of mol.: 2 / Mutation: T3N
Source method: isolated from a genetically manipulated source
Details: T3N mutant / Source: (gene. exp.) Escherichia coli KLY (bacteria)
Gene: orf6, vapB, ACN81_23035, FGAF1022_52390, FGAS143_47180, G4A38_21185, G4A47_21035
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7B3V0
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M Lithium sulphate monohydrate, 0.1 M sodium citrate tribasic dihydrate, 26 % PEG200
PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979261 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979261 Å / Relative weight: 1
ReflectionResolution: 2.5→44.5 Å / Num. obs: 18721 / % possible obs: 99.9 % / Redundancy: 10.07 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.098 / Net I/σ(I): 13.21
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.5-2.575.79613760.2156.1041
2.57-2.645.33513140.2085.6141
2.64-2.713.50812920.3413.6921
2.71-2.82.43912710.4862.5671
2.8-2.891.90412100.5932.0051
2.89-2.991.23111690.7841.2961
2.99-3.10.90411460.8250.9521
3.1-3.230.59311080.9310.6241
3.23-3.370.37510610.9680.3951
3.37-3.540.27310100.9860.2881
3.54-3.730.1629580.9950.1711
3.73-3.950.1179120.9960.1231
3.95-4.230.0878640.9970.0921
4.23-4.570.0648040.9980.0681
4.57-50.0537570.9990.0561
5-5.590.0536860.9990.0561
5.59-6.460.0516060.9990.0541
6.46-7.910.0375170.9990.0391
7.91-11.190.0294170.9990.031
11.19-44.50.0262430.9990.0281

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(1.20.1_4487: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→44.49 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2842 753 4.78 %
Rwork0.2309 --
obs0.2334 15769 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 0 0 3159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073210
X-RAY DIFFRACTIONf_angle_d0.9314335
X-RAY DIFFRACTIONf_dihedral_angle_d6.094439
X-RAY DIFFRACTIONf_chiral_restr0.055486
X-RAY DIFFRACTIONf_plane_restr0.009572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.850.39681220.34812972X-RAY DIFFRACTION100
2.86-3.140.3651850.34972899X-RAY DIFFRACTION100
3.14-3.60.33011440.29482998X-RAY DIFFRACTION100
3.6-4.530.25371220.22123034X-RAY DIFFRACTION100
4.53-44.490.26961800.19873113X-RAY DIFFRACTION100

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